That does not mean that the ENTIRE hull is covered in armor - armor is mounted in belts, the ship has a belt of armor along each side and (apparently - according to wiki) along the top and bottom - which would be a useless waste of mass since the weight of this armor could be moved to the sides and add more protection where incoming fire is likely to impact instead of protecting a non-target area, anyway, there would still be sections of the hull between the belts that would be unarmored - not a burrito-wrap of armor all the way around - talk about a complete waste of mass.
Okay. Even if we grant all that, even if we assume that it is not only possible but actually practical to dig into an SD, rip out all the main battery missile mounts and their magazines and replace them with something capable of firing useful munitions, or at the very least replace the fire control equipment with stuff that can interface with pod-based weaponry, the big question standing in the room is still whether the economic and strategic situation warrants doing this.
And that's just for a simple case of rebuilding an SD into something analoguous to the Nike BC(L)'s, i.e. a ship capable of firing useful salvoes of MDMs from internal magazines (which is something that Manticore
actually did do on a few Gryphons, if I recall correctly, before deciding that the cost involved compares badly to just building more SD(P)s).
Skimper has repeatedly suggested rebuilding these ships into something
completely different, like fitting them with substantial LAC carrying capability. The books tell us, explicitly, that CLACs are built with a completely different layout of the spaces outside their core hull compared to a classical Superdreadnought, there is substantial work to be done if they are supposed to launch LACs in a practical way (i.e. without having to shut down their own wedge while doing so). They also tell us that, for similar reasons, building ships with internal pod magazines requires a substantial rethinking of the placement of internal components.
These are all things that are undoubtedly possible to do, assuming that there is literally nothing better that the shipyards and their workers could be doing instead. But that is really, really not the case in the Honorverse at the moment. These proposed projects all fail the simple question of what would be more practical: Either build a completely new ship, or refurbish these old ones. You can't really do both.
finally the ships weapons have to be able to fire OUT of the armor, the hull, though armored over much of the area CANNOT be armored where weapons or sensors (or nodes etc...) are mounted those section of the ship are unarmored and can be used to remove the same equipment that is suppose to extend through it anyway. the Burrito-wrap ship you suggest would be an inefficient combat vessel with limited armor where its actually needed, superfluous protection where it can do no good in a normal engagement and be impossible to repair after an engagement, since all of your equipment is so block off by armor that you can't remove damage (or even worn-out) equipment after a battle or even during refits or mid-life upgrades. all ships are designed to be able to be refit and upgraded with limited underfinance from the ships own structure. How did they get the equipment in-place in the first place?
You need to be aware of a few things which you apparently haven't realized. The ships you are talking about were all built and designed in an era where combat paradigms had essentially stabilized. For 200 years or more (I think the Scientist class dates that far back?), there were no significant advances that substantially altered the combat environment (the last significant advance, the laser head, could be addressed with a comparatively minor update to the point defence and EW suites of the ships involved). The major systems on board these ships, the main energy battery weapons and missile launchers and their assorted support structures, literally did not need to be changed at all in order to keep these ships viable in combat.
So, with that in mind, it is entirely possible for SLN naval designers to build these systems in a way that would make replacement harder, but make the ships more resilient over all, which would certainly fit in with the mindset these people were operating under.